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#!/usr/bin/python3 -O
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import sys
import os
import re
if len(sys.argv) < 2:
print("Misassembled contigs getter: prints IDs of misassembled contigs or save these contigs in fasta (if input contigs file and output file specified)")
print("Usage: " + sys.argv[0] + " <plantagota output> [input_contigs.fasta misassembled_contigs.fasta]")
sys.exit()
in_file = open(sys.argv[1], "r")
basename, ext = os.path.splitext(sys.argv[1])
out_IDs_filename = basename + ".txt.mis"
out_aligns_filename = basename + ".aligns"
out_IDs_file = open(out_IDs_filename, "w")
out_aligns_file = open(out_aligns_filename, "w")
mis_contigs_ids = []
mis_contigs_aligns = []
#skipping prologue
for line in in_file:
if line.startswith("Analyzing contigs..."):
break
# main part of plantagora output
cur_contig_id = ""
cur_contig_align = ""
was_extensive_mis = False
for line in in_file:
if line.startswith("Analyzing coverage..."):
break
if line.startswith(" CONTIG:"):
cur_contig_id = line.split(" CONTIG:")[1].strip()
if was_extensive_mis:
was_extensive_mis = False
mis_contigs_aligns.append(cur_contig_align)
cur_contig_align = ""
cur_contig_align += line
if (line.find("Extensive misassembly") != -1) and (cur_contig_id != ""):
was_extensive_mis = True
mis_contigs_ids.append(cur_contig_id.split()[0])
cur_contig_id = ""
if was_extensive_mis:
mis_contigs_aligns.append(cur_contig_align)
# printing IDs of misassembled contigs
print "IDs of misassembled contigs saved in " + out_IDs_filename
for contig_id in mis_contigs_ids:
out_IDs_file.write(contig_id + '\n')
print "Alignments of misassembled contigs saved in " + out_aligns_filename
for contig_align in mis_contigs_aligns:
out_aligns_file.write(contig_align)
in_file.close()
out_IDs_file.close()
out_aligns_file.close()
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